Perhaps bob could answer the following questions about his method of "analysis":
1. On what basis do you select animals for the "mammal group". Is this a priori selection going to bias your results?
It is hard to see how this would bias the results since I have other charts that include
all the creatures (fish, reptiles, amphibians, birds, etc) for which cyto c sequences are known and it doesn't seem to affect any conclusions drawn by simply viewing the color coded charts
2. Why do you do the analysis at the level of "mammal" and not at a higher (e.*., vertebrate) or lower (e.*., primates/rodents/etc.) level?
First, there is no "analysis" involved. I present the sequences in their raw form with only the differences highlighted to make it easier to see what is going on between the various organism cyto c. Also as I mentioned above the groups seem to "fall out" naturally so it is logical to view them separately before comparing one group to another.
3. What is your view on the demonstrated fact that the composition of the "common mammal" is heavily influenced by the dominant subgroup of animals? Is this a flaw in the method?
I don't agree that what you have said is true. The reason becomes more obvious when a larger number of animals is viewed in a more comprehensive chart. The orginal chart published by Dobyzansky, et. al. and used in many biology classes even today is similar to what I posted on the Web, but has only 22 creatures on it including representatives from plant, fish, fungi, insect, etc. The common mammal could still be determined from the few mammals on that chart alone and this result stayed essentially the same even when I found and added 11 more mammal sequences to that chart. The only positions in any doubt for mammals are two, 70 and 100. If one looks at other groups of animals those two positions can be resolved because most of the other animals agree with one or the other of the two alternative amino acids. If you like I will change the chart to the alternate amino acid, but this will change none of the conclusions one can make by simply looking at the data. Mice will still be quite distinct from men, more than can be explained by random mutation of the amino acids within the protein.
If you don't believe me look at this chart where I used the alternate amino acid as the "common mammal":
http://members.aol.com/Bobsbend/cytoca.htm
4. Why have you done the analysis this way? What predictions are you testing from evolutionary theory or creationism? How are the predictions tested by the analysis?
I have done no analysis. The data has been left as the raw amino acid sequences of the protein cytochrome c. It has not been altered in any way except that I highlighted those amino acid differences from the most commonly occurring one at each of the various positions.
The evidence speaks for itself in the sense that each person is free to draw whatever conclusions they feel are justified from the data itself. In my own case I find it illogical to believe that all mammals could have been derived from a common ancestor because several of the currently existing forms have sequences that are too close to what that common ancestor would have had to have as a protein sequence. This is despite the fact that all of the creatures would of necessity had the same length of time to diverge by random mutation from that same common ancestor.
What I am saying is that if the cow/pig/sheep sequence was the same as the common ancestor why did mutations not affect their sequence?
Why are the primates so different than other mammals?
Why are mice so different?
Why are whales the same as camels?
) as the basal lineage are not even represented.